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Coexpression cluster:C4424: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280739938661754!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321923543092241!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173462360395867!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066699575322773!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310307328284806!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00800267247276998!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330676701715282!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390139102179534
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280739938661754!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321923543092241!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173462360395867!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066699575322773!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310307328284806!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00800267247276998!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330676701715282!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390139102179534
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}}
}}

Revision as of 16:44, 26 November 2012


Full id: C4424_somatostatinoma_pineal_neuroectodermal_retina_thyroid_Mesenchymal_left



Phase1 CAGE Peaks

Hg19::chr4:75858290..75858299,+p3@PARM1
Hg19::chr4:75858318..75858339,+p1@PARM1
Hg19::chr4:75858349..75858360,+p2@PARM1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
lymphocyte of B lineage2.96e-0824
pro-B cell2.96e-0824
Uber Anatomy
Ontology termp-valuen
adult organism1.80e-48114
neural tube2.51e-1956
neural rod2.51e-1956
future spinal cord2.51e-1956
neural keel2.51e-1956
regional part of nervous system2.97e-1853
regional part of brain2.97e-1853
regional part of forebrain4.20e-1841
forebrain4.20e-1841
anterior neural tube4.20e-1841
future forebrain4.20e-1841
neurectoderm5.40e-1886
neural plate1.03e-1682
presumptive neural plate1.03e-1682
central nervous system2.09e-1681
nervous system1.64e-1589
pre-chordal neural plate1.30e-1461
brain grey matter2.26e-1434
gray matter2.26e-1434
telencephalon2.89e-1434
cerebral hemisphere6.20e-1432
organ system subdivision1.17e-13223
regional part of telencephalon1.71e-1332
regional part of cerebral cortex3.91e-1322
brain7.40e-1368
future brain7.40e-1368
neocortex1.81e-1220
ecto-epithelium1.79e-11104
structure with developmental contribution from neural crest6.45e-11132
cerebral cortex1.81e-1025
pallium1.81e-1025
multi-tissue structure6.53e-10342
ectoderm-derived structure1.41e-09171
ectoderm1.41e-09171
presumptive ectoderm1.41e-09171
anatomical cluster2.69e-08373


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0280739938661754
EGR1#195834.988179094810140.008056488137383440.0321923543092241
PAX5#507936.669565531177830.003370290999677260.0173462360395867
RAD21#5885310.35503389545630.0009004912073565420.0066699575322773
SMC3#9126315.04493284493280.0002935825420371870.00310307328284806
SUZ12#23512233.41052060737530.00117826764536030.00800267247276998
YY1#752834.911170749853860.008441455341808260.0330676701715282
ZNF143#7702313.50087655222790.0004062804962997170.00390139102179534



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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